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| #(1) Setup paths and environment. | |
| library(BTR) | |
| library(doParallel) | |
| path='~/btr_output/' | |
| setwd(path) | |
| #Setting up for parallel processing. | |
| registerDoParallel(cores=4) | |
| #(2)Load data. | |
| data(bon_bmodel) | |
| data(bon_istate) | |
| data(wilson_raw_rnaseq) | |
| bmodel = initialise_model(bon_bmodel) | |
| istate = initialise_data(bon_istate) | |
| #(3)Filtering expression data. | |
| cdata = initialise_raw_data(wilson_raw_rnaseq) #do not filter data at this stage. keep the whole matrix. | |
| fcdata = cdata[grepl('hsc', rownames(cdata)),] #select only HSC cells. | |
| #(3)Filtering expression data. | |
| result = model_train(cdata=fcdata, bmodel=bmodel, istate=istate, verbose=T) | |
| filename = 'bon_wilson_rnaseq_HSC_trained_bmodel.rda' | |
| save(result, file=filename) | |
| #Cleaning up. | |
| stopImplicitCluster() |